Note we don't (yet) have official 64 bit Windows Installers - however, Christoph Gohlke has

Note we don't (yet) have official 64 bit Windows Installers - however, Christoph Gohlke has

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=== Installation Instructions ===

=== Installation Instructions ===

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For Windows we provide click-and-run installers (specific to your version of python), but you will first need to install some prerequisite software (listed below, in particular, NumPy).

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For '''Windows''' we provide click-and-run installers (specific to your version of python), but you will first need to install some prerequisite software (listed below, in particular, NumPy).

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Most Linux distributions will include an optional Biopython package (described below), and will take care of any prerequisite software automatically.

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For Mac OS X, we recommend installing from source (see below). Under (Snow) Leopard, you will need to have installed Apple's XCode tools ''including'' the optional 10.4 SDK (check the option for 10.4 support when installing Xcode tools) which comes on DVD with the computer. For Lion, just install XCode from the Apple App Store (it is a big download).

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Otherwise you typically install from source by downloading and uncompressing the archive, then running the commands:

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Most '''Linux''' distributions will include an optional Biopython package (described below), and will take care of any prerequisite software automatically. Otherwise you typically install from source by downloading and uncompressing the archive, then running the commands:

For '''Mac OS X''', we recommend installing from source as above. You will need to have installed Apple's XCode tools from the App Store (it is a big download), and then the optional command line tools from within the XCode GUI's options menu, or on Mavericks by using the command:

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xcode-select --install

If you have trouble, see the full installation instructions:

If you have trouble, see the full installation instructions:

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=== Required Software ===

=== Required Software ===

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* [http://www.python.org Python 2.5, 2.6 or 2.7] (Biopython 1.56 was the last release to officially support Python 2.4, although Biopython 1.58 should work)

* [http://www.python.org/doc/current/inst/inst.html C compiler (if compiling from source)] You need a C compiler supported by distutils, gcc will work fine on UNIX-like platforms. This is not needed on Windows if using the install programs provided above. On Mac OS, we recommend you install Apple's XCode ''including'' the 10.4 SDK if offered.

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* [http://www.python.org/doc/current/inst/inst.html C compiler (if compiling from source)] You need a C compiler supported by distutils, gcc will work fine on UNIX-like platforms. This is not needed on Windows if using the install programs provided above. On Mac OS, you should install Apple's XCode ''including'' the command line tools.

* [http://numpy.scipy.org/ NumPy (Numerical Python)]. Note that until Biopython 1.49, Biopython used the older Numeric library. We have tested NumPy 1.1 to 1.5 with Biopython.

* [http://numpy.scipy.org/ NumPy (Numerical Python)]. Note that until Biopython 1.49, Biopython used the older Numeric library. We have tested NumPy 1.1 to 1.5 with Biopython.

=== Optional Software ===

=== Optional Software ===

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For compiling Biopython:

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* [http://flex.sourceforge.net/ flex: The Fast Lexical Analyzer] -- for building Bio.PDB.mmCIF.MMCIFlex which is used to parse macromolecular Crystallographic Information Files (mmCIF)

Some parts of Biopython use the following additional python libraries:

Some parts of Biopython use the following additional python libraries:

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sudo apt-get build-dep python-biopython

sudo apt-get build-dep python-biopython

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Note: You may need to additionally install the NumPy package by hand, as a very out of date repository may still expect Biopython to use Numeric instead.

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=== Archlinux ===

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Biopython is in the [https://www.archlinux.org/packages/?q=biopython official Archlinux repository] as python-biopython (for Python 3) or python2-biopython (for Python 2) and can be installed using pacman:

Note we don't (yet) have official 64 bit Windows Installers - however, Christoph Gohlke has
kindly made Windows 64bit installers for
NumPy and Biopython (and other tools) available for testing.

Installation Instructions

For Windows we provide click-and-run installers (specific to your version of python), but you will first need to install some prerequisite software (listed below, in particular, NumPy).

Most Linux distributions will include an optional Biopython package (described below), and will take care of any prerequisite software automatically. Otherwise you typically install from source by downloading and uncompressing the archive, then running the commands:

For Mac OS X, we recommend installing from source as above. You will need to have installed Apple's XCode tools from the App Store (it is a big download), and then the optional command line tools from within the XCode GUI's options menu, or on Mavericks by using the command:

Required Software

C compiler (if compiling from source) You need a C compiler supported by distutils, gcc will work fine on UNIX-like platforms. This is not needed on Windows if using the install programs provided above. On Mac OS, you should install Apple's XCode including the command line tools.

NumPy (Numerical Python). Note that until Biopython 1.49, Biopython used the older Numeric library. We have tested NumPy 1.1 to 1.5 with Biopython.

Optional Software

Some parts of Biopython use the following additional python libraries:

Easy Install

We don't officially sanction this option, but it has been reported to work fine.
If you have easy_install installed on your computer, you can download and install the latest Biopython distribution by simply executing this command:

easy_install -f http://biopython.org/DIST/ biopython

You will have to have administrator's rights to do this. On a Unix style system this is normally done by:

sudo easy_install -f http://biopython.org/DIST/ biopython

Packages

For those of you using Linux, the easiest way to install Biopython is through your distribution's package management system. However, unless you are running a recent release of your Linux Distribution, you may find that the Biopython packages available to be a little out of date. You might want to see if there is a backport available, otherwise you will have to install Biopython from source.

Ubuntu or Debian

You should be able to install Biopython and its dependencies using the Synaptic GUI tool (on the main menu under System / Administration / Synaptic Package Manager), or at the command line using:

However, this will probably not be the latest release (see Ubuntu listing here, and Debian listing here). If you want the latest version of Biopython, you will need to install it from source. However, you should be able to automatically install the build dependencies with the following command:

sudo apt-get build-dep python-biopython

Archlinux

Biopython is in the official Archlinux repository as python-biopython (for Python 3) or python2-biopython (for Python 2) and can be installed using pacman:

pacman -S python2-biopython

Or, for Python 3:

pacman -S python-biopython

Fedora

Biopython is an official Fedora package (since Fedora 5). The package is named python-biopython, and can be installed using yum as root:

yum install python-biopython

or via one of the GUI package management systems such as pirut and PackageKit (available in F-9 and later).

Gentoo Linux

Gentoo's portage tree contains an ebuild (sci-biology/biopython) which builds from source. To install it, open a terminal as root and run:

emerge -va biopython

Here is a link to Biopython at Gentoo-Portage which shows the latest versions in Gentoo's Portage tree.

Ports

FreeBSD

The most easy way of installing Biopython in FreeBSD is through the Ports Collection. If you're new to this procedure please take a look at this document. Supposing that you're familiar with this method and that you have an up-to-date ports tree, all you need to do is to execute the following commands as root:

cd/usr/ports/biology/py-biopython
makeinstall clean

Due to the great architecture of the ports system, this simple commands will automatically fetch and install Biopython (as well as its necessary dependencies).

Please note that Biopython 1.48 and older require the Numeric library, not its replacement NumPy. Windows installers for Python 2.4 and older are available from the Numerical Python website. A Windows installer for Numeric 24.2 for Python 2.5 is available here: Numeric-24.2.win32-py2.5.exe 446 Kb

Please note that Biopython 1.48 and older used mxTextTools 2.0 in some of the parsers. There were a few niggles with mxTextTools 3.0, so ideally install the older mxTextTools 2.0.